Biomarker Development Pipeline

The concept of a pipeline illustrates the process of biomarker development (Figure 1). The pipeline uses a combination of technologies to capture molecular information about cancers and refine that information to select protein markers that most reliably detect disease.

The pipeline begins with Discovery--an unbiased analysis of normal and cancer tissue specimens to identify differences in collections of tissue proteins. Discovery analyses are performed on a small number of very well-characterized cancers, precancers or normal tissue specimens. The analyses are done by shotgun proteomics with liquid chromatography-tandem mass spectrometry (LC-MS/MS), using a method that is carefully standardized to ensure consistent performance. Although the analyses can detect thousands of proteins, only a small fraction (~100-200) may differ between normal and cancer tissue. These proteins are biomarker candidates, which are further evaluated in the next stage of the pipeline. Prior to further evaluation, other information such as gene expression patterns, mutations or emerging understanding of relevant cancer biology helps to prioritize candidates for further evaluation.

The objective of the next stage is to reduce this large list of biomarker candidates to identify a much smaller number of the highest quality candidates. Candidates are subjected to an iterative process of Verification and Assay Development, in which highly sensitive, targeted analyses confirms their presence in tissues or plasma. Some of the candidates may be directly detected by targeted LC-MS/MS analyses. Other candidates will only be detected by first using antibodies to capture the candidate proteins, followed by targeted LC-MS/MS analyses to achieve high sensitivity detection. This requires the development of antibodies to biomarker candidates. Biomarker candidates that emerge from this stage of the pipeline can be measured accurately with sensitive, reliable methods and are proven to differ in levels in plasma and/or tissues in “gold standard” specimens of patients with and without cancer.

The final stage of the pipeline is evaluation of biomarker candidates in clinical trials in a context most relevant to their eventual clinical application. A relatively small number (<20) of highly credentialed biomarker candidates are evaluated in clinical trials. The objective of these trials is Validation, which evaluates not only the the performance of the biomarker candidates in a test to accurately detect disease, but also the ability of the test to provide a beneficial impact on health outcomes for patients.